Re: [AMBER] energy minimum vs binding pose for charge calculation

From: David A Case <>
Date: Wed, 1 Nov 2017 13:56:07 -0400

On Wed, Nov 01, 2017, Thomas Evangelidis wrote:
> QMMM: Unable to achieve self consistency to the tolerances specified
> QMMM: No convergence in SCF after 1000 steps.
> QMMM: E = -0.1893E+07 DeltaE = 0.1983E+00 DeltaP = 0.3701E-01
> QMMM: Smallest DeltaE = 0.1041E-06 DeltaP = 0.9668E-04 Step = 98
> One solution would be to increase the scfconv from 1.d-10 to 1.d-8 and grms_
> tol from 0.0005 to 0.005 inside file. Btw, is it possible to pass
> these settings directly to Antechamber instead of amber16/bin/sqm?

Yes: use the "-ek" parameter in antechamber, which will put that information
in the file. See Notes 6 and 7 of Section 15.2 of the Reference

> The other option could be to pass energy minimized geometries to
> antechamber. Currently, I pass the binding poses, which sometimes differ
> substantially from the energy minimum. However, assuming that antechamber
> finishes successfully, which charges would be better for simulating the
> protein-ligand complex, those calculated using the energy minimum or those
> calculated using the real binding pose of the ligand?

If it makes a difference, you might want to consider multi-conformer fits.
Note that you can turn off minimization via the "-ek" flag, if you wish
to use the input geometry.


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Received on Wed Nov 01 2017 - 11:00:03 PDT
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